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\documentclass{oxthesis}

\usepackage[acronym, nonumberlist]{glossaries} 

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% citations and references
\usepackage[backend=biber,style=authoryear-icomp, firstinits=true, maxcitenames=3, sorting=ynt]{biblatex}
%\usepackage{cite}
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\addbibresource{reference.bib}


\makeglossaries
 
 
\newglossaryentry{archetype}
{
	name=archetype,
	description={An archetype is a re-usable, formal model of a medical domain concept 
	that expresses constraints on an underlying reference model}
}

\newglossaryentry{sem-inter}
{
	name=semantic interoperability,
	description={The ability of computer systems to communicate and exchange information that can be interpreted correctly 
	and meaningfully}
}

\newglossaryentry{clin-term}
{
	name=clinical terminology,
	description={A controlled vocabulary or code system that provides a set of formally defined concepts in the medical
	domain}
}

\newglossaryentry{ref-mod}
{
	name=reference model,
	description={An information model that provides the fundamental building blocks of an EHR}
}


\newglossaryentry{dl}
{
	name=description logic,
	description={A family of formal knowledge representation languages}
}

\newglossaryentry{im}
{
	name=information model,
	description={A representation of a domain's data and schemas}
}


\newglossaryentry{openehr}
{
	name=openEHR,
	description={The openEHR Foundation is an international not-for-profit foundation working on health informatics}
}

\newglossaryentry{term-binding}
{
	name=terminology binding,
	description={The mechanism to associate terms in the information model with clinical concepts}
}

\newglossaryentry{ontology}
{
	name=ontology,
	description={A purpose driven systematic representation of domain concepts and their relationships to other concepts}
}

\newacronym{ehr}{EHR}{Electronic Health Record}
\newacronym{cen}{CEN}{Comit\'{e} Europ\'{e}en de Normalisation}
\newacronym{hl7}{HL7}{Health Level 7}
\newacronym{rm}{RM}{Reference Model}
\newacronym{aom}{AOM}{Archetype Object Model}
\newacronym{api}{API}{Application Programming Interface}
\newacronym{ckm}{CKM}{Clinical Knowledge Manager}
\newacronym{adl}{ADL}{Archetype Deﬁnition Language}
\newacronym{cda}{CDA}{Clinical Document Architecture}
\newacronym{cts}{CTS}{Common Terminology Services}
\newacronym{icd}{ICD}{International Classification of Diseases and Related Health Problems}
\newacronym{ihtsdo}{IHTSDO}{International Health Terminology Standards Development Organisation}
\newacronym{iso}{ISO}{International Organization of Standardization}
\newacronym{en13606}{EN13606}{ISO-13606 Health informatics - Electronic Health Record Communication Standard}
\newacronym{loinc}{LOINC}{Logical Observation Identifiers names and Codes}
\newacronym{snomed-ct}{SNOMED-CT}{Systemized Nomenclature of Medicine - Clinical Terms}
\newacronym{uml}{UML}{Unified Modelling Language}
\newacronym{owl}{OWL}{Web Ontology Language}

%-------------front matter--------------

\title{Terminological Shadows: a framework to integrate Electronic Health Records
with Clinical Terminologies}

	%\title{My awesome thesis\\[1ex]     %your thesis title,
        %title bla bla}   %note \\[1ex] is a line break in the title

	\author{Sheng Yu}             %your name
	\college{School of Electrical Engineering Systems}  %your college

	%\renewcommand{\submittedtext}{change the default text here if needed}
	\degree{Doctor of Philosophy}     %the degree
	\degreedate{Supervisor: Dr Damon Berry, Dr Jes\'{u}s Bisbal}         
	%end the preamble and start the document

\begin{document}
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\include{declaration}        % include a dedication.tex file
\include{acknowlegements}   % include an acknowledgements.tex file
\include{abstract}          % include the abstract

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\include{Chapter1} 
\include{chapter2} 
\include{chapter3} 
\include{chapter4} 
\include{shadowchapter} 
\include{results} 
\include{apply} 
\include{conclusion} 




%next line adds the Bibliography to the contents page
%change 'Bibliography' to 'References' if needed
\addcontentsline{toc}{chapter}{Bibliography}

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\glsaddall
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